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- EMDB-4995: Subtomogram average of a part of the rabies lyssavirus ribonucleo... -

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Basic information

Entry
Database: EMDB / ID: EMD-4995
TitleSubtomogram average of a part of the rabies lyssavirus ribonucleoprotein
Map data
Sample
  • Virus: Rabies virus
Biological speciesRabies virus
Methodsubtomogram averaging / cryo EM / Resolution: 15.0 Å
AuthorsRiedel C / Vasishtan D / Prazak V / Ghanem A / Conzelmann K-K / Ruemenapf T
CitationJournal: Sci Rep / Year: 2019
Title: Cryo EM structure of the rabies virus ribonucleoprotein complex.
Authors: Christiane Riedel / Daven Vasishtan / Vojtěch Pražák / Alexander Ghanem / Karl-Klaus Conzelmann / Till Rümenapf /
Abstract: Rabies virus is an important zoonotic pathogen. Its bullet shaped particle contains a helical nucleocapsid. We used cryo-electron tomography and subsequent subtomogram averaging to determine the ...Rabies virus is an important zoonotic pathogen. Its bullet shaped particle contains a helical nucleocapsid. We used cryo-electron tomography and subsequent subtomogram averaging to determine the structure of its ribonucleoprotein. The resulting electron density map allowed for confident fitting of the N-protein crystal structure, indicating that interactions between neighbouring N-proteins are only mediated by N- and C-terminal protruding subdomains (aa 1-27 and aa 355-372). Additional connecting densities, likely stabilizing the ribonucleoprotein complex, are present between neighbouring M-protein densities on the same helical turn and between M- and N-protein densities located on neighbouring helical turns, but not between M-proteins of different turns, as is observed for the related Vesicular stomatitis virus (VSV). This insight into the architecture of the rabies virus nucleocapsid highlights the surprising structural divergence of large biological assemblies even if the building blocks - here exemplified by VSV M- and N-protein - are structurally closely related.
History
DepositionMay 22, 2019-
Header (metadata) releaseMay 29, 2019-
Map releaseJul 10, 2019-
UpdateJul 17, 2019-
Current statusJul 17, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4995.png

Downloads & links

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Map

FileDownload / File: emd_4995.map.gz / Format: CCP4 / Size: 844.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.35 Å/pix.
x 60 pix.
= 201.12 Å		3.35 Å/pix.
x 60 pix.
= 201.12 Å		3.35 Å/pix.
x 60 pix.
= 201.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.352 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5 / Movie #1: 4.5
Minimum - Maximum0.3004837 - 10.78492
Average (Standard dev.)4.2021585 (±0.9374101)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions606060
Spacing606060
CellA=B=C: 201.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.3523.3523.352
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z201.120201.120201.120
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS606060
D min/max/mean0.30010.7854.202

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Supplemental data

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Sample components

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Entire : Rabies virus

EntireName: Rabies virus
Components
  • Virus: Rabies virus

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Supramolecule #1: Rabies virus

SupramoleculeName: Rabies virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 11292 / Sci species name: Rabies virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host systemOrganism: Homo sapiens (human) / Recombinant cell: HEK293T

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 7079
ExtractionNumber tomograms: 10 / Number images used: 7079
Final angle assignmentType: NOT APPLICABLE

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